Runtime reflection error when using JSON output format

[ejseqera]

When trying to list organizations or workspaces with JSON output format (tw -o json organizations list), the command fails with a GraalVM native-image reflection registration error.

The command fails with the following error:

Exception in thread "main" org.graalvm.nativeimage.MissingReflectionRegistrationError: The program tried to reflectively invoke method public java.lang.String io.seqera.tower.model.OrgType.getValue() without it being registered for runtime reflection. Add public java.lang.String io.seqera.tower.model.OrgType.getValue() to the reflection metadata to solve this problem. See https://www.graalvm.org/latest/reference-manual/native-image/metadata/#reflection for help.
        at org.graalvm.nativeimage.builder/com.oracle.svm.core.reflect.MissingReflectionRegistrationUtils.forQueriedOnlyExecutable(MissingReflectionRegistrationUtils.java:83)
        at java.base@21.0.6/java.lang.reflect.Method.acquireMethodAccessor(Method.java:77)
        at java.base@21.0.6/java.lang.reflect.Method.invoke(Method.java:577)
        at com.fasterxml.jackson.databind.introspect.AnnotatedMethod.getValue(AnnotatedMethod.java:183)
        at com.fasterxml.jackson.databind.ser.std.JsonValueSerializer.serialize(JsonValueSerializer.java:166)
        at com.fasterxml.jackson.databind.ser.BeanPropertyWriter.serializeAsField(BeanPropertyWriter.java:727)
        at com.fasterxml.jackson.databind.ser.std.BeanSerializerBase.serializeFields(BeanSerializerBase.java:722)
        at com.fasterxml.jackson.databind.ser.BeanSerializer.serialize(BeanSerializer.java:166)
        at com.fasterxml.jackson.databind.ser.impl.IndexedListSerializer.serializeContents(IndexedListSerializer.java:119)
        at com.fasterxml.jackson.databind.ser.impl.IndexedListSerializer.serialize(IndexedListSerializer.java:79)
        at com.fasterxml.jackson.databind.ser.impl.IndexedListSerializer.serialize(IndexedListSerializer.java:18)
        at com.fasterxml.jackson.databind.ser.BeanPropertyWriter.serializeAsField(BeanPropertyWriter.java:727)
        at com.fasterxml.jackson.databind.ser.std.BeanSerializerBase.serializeFields(BeanSerializerBase.java:722)
        at com.fasterxml.jackson.databind.ser.BeanSerializer.serialize(BeanSerializer.java:166)
        at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider._serialize(DefaultSerializerProvider.java:480)
        at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:319)
        at com.fasterxml.jackson.databind.ObjectWriter$Prefetch.serialize(ObjectWriter.java:1433)
        at com.fasterxml.jackson.databind.ObjectWriter._configAndWriteValue(ObjectWriter.java:1135)
        at com.fasterxml.jackson.databind.ObjectWriter.writeValueAsString(ObjectWriter.java:1005)
        at io.seqera.tower.cli.utils.JsonHelper.prettyJson(JsonHelper.java:29)
        at io.seqera.tower.cli.utils.ResponseHelper.outputFormat(ResponseHelper.java:52)
        at io.seqera.tower.cli.commands.AbstractApiCmd.call(AbstractApiCmd.java:450)
        at io.seqera.tower.cli.commands.AbstractApiCmd.call(AbstractApiCmd.java:70)
        at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
        at picocli.CommandLine.access$1300(CommandLine.java:145)
        at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)
        at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
        at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)
        at picocli.CommandLine.execute(CommandLine.java:2078)
        at io.seqera.tower.cli.Tower.main(Tower.java:103)
        at java.base@21.0.6/java.lang.invoke.LambdaForm$DMH/sa346b79c.invokeStaticInit(LambdaForm$DMH)

Version info:

tw info

    Details
    -------------------------+-----------------------------
     Tower API endpoint      | https://api.cloud.seqera.io 
     Tower API version       | 1.37.0                      
     Tower version           | 25.1.0-cycle5               
     CLI version             | 0.11.2 (2a4e8d5)            
     CLI minimum API version | 1.38.0                      
     Authenticated user      | eshajoshi                   

    System health status
    ---------------------------------------+--------
     Remote API server connection check    | OK     
     Tower API version check               | FAILED 
     Authentication API credential's token | OK     

    Tower API version is 1.37.0 while the minimum required version to be fully compatible is 1.38.0

• JDK version: 21.0.6
• OS: MacOS M2

[ejseqera]

@georgi-seqera Looks like a similar issue still persists for the Linux dist when running tw studios add command in 0.11.3:

 tw studios add --name rstudio_environment --description 'An RStudio environment for seqerakit e2e testing' --workspace seqerakit-e2e/showcase --template public.cr.seqera.io/platform/data-studio-rstudio:4.4.1-u1-0.7 --compute-env seqera_aws_virginia_fusionv2_nvme  --cpu 2 --memory 4096 --mount-data-uris s3://seqeralabs-showcase  --labels project=seqerakit-e2e,organization=seqerakit-e2e,study=showcase
Exception in thread "main" org.graalvm.nativeimage.MissingReflectionRegistrationError: The program tried to reflectively invoke method public void io.seqera.tower.model.DataStudioTemplate.setStatus(io.seqera.tower.model.DataStudioVersionStatus) without it being registered for runtime reflection. Add public void io.seqera.tower.model.DataStudioTemplate.setStatus(io.seqera.tower.model.DataStudioVersionStatus) to the reflection metadata to solve this problem. See https://www.graalvm.org/latest/reference-manual/native-image/metadata/#reflection for help.
	at org.graalvm.nativeimage.builder/com.oracle.svm.core.reflect.MissingReflectionRegistrationUtils.forQueriedOnlyExecutable(MissingReflectionRegistrationUtils.java:83)
	at java.base@21.0.7/java.lang.reflect.Method.acquireMethodAccessor(Method.java:77)
	at java.base@21.0.7/java.lang.reflect.Method.invoke(Method.java:577)

Versions:

$ tw info

    Details
    -------------------------+-----------------------------
     Tower API endpoint      | https://api.cloud.seqera.io
     Tower API version       | 1.37.0
     Tower version           | 25.1.0-cycle5
     CLI version             | 0.11.3 (4124d83)
     CLI minimum API version | 1.37.0
     Authenticated user      | eshajoshi

    System health status
    ---------------------------------------+----
     Remote API server connection check    | OK
     Tower API version check               | OK
     Authentication API credential's token | OK

$ hostnamectl
   Static hostname: ip-172-31-35-124.ec2.internal
         Icon name: computer-vm
           Chassis: vm
        Machine ID: ff1d98459c0e4718bc888c965abd7e9d
           Boot ID: d35c285f74874e7ab0d55b949991b66c
    Virtualization: xen
  Operating System: Amazon Linux 2
       CPE OS Name: cpe:2.3:o:amazon:amazon_linux:2
            Kernel: Linux 5.10.149-133.644.amzn2.x86_64
      Architecture: x86-64

Same command works fine on MacOS:

tw studios add --name rstudio_environment --description 'An RStudio environment for seqerakit e2e testing' --workspace seqerakit-e2e/showcase --template public.cr.seqera.io/platform/data-studio-rstudio:4.4.1-u1-0.7 --compute-env seqera_aws_virginia_fusionv2_nvme  --cpu 2 --memory 4096 --mount-data-uris s3://seqeralabs-showcase  --labels project=seqerakit-e2e,organization=seqerakit-e2e,study=showcase 

  Studio aa0c5cd9 CREATED at [seqerakit-e2e / showcase] workspace.

Version info on Mac:

$ tw info

    Details
    -------------------------+-----------------------------
     Tower API endpoint      | https://api.cloud.seqera.io 
     Tower API version       | 1.37.0                      
     Tower version           | 25.1.0-cycle5               
     CLI version             | 0.11.3 (4124d83)            
     CLI minimum API version | 1.37.0                      
     Authenticated user      | eshajoshi                   

    System health status
    ---------------------------------------+----
     Remote API server connection check    | OK 
     Tower API version check               | OK 
     Authentication API credential's token | OK 

$ uname -a
Darwin Mac 24.4.0 Darwin Kernel Version 24.4.0: Fri Apr 11 18:33:46 PDT 2025; root:xnu-11417.101.15~117/RELEASE_ARM64_T8112 arm64